Multiple sequence alignment - TraesCS2D01G197200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G197200 chr2D 100.000 4189 0 0 1 4189 143895947 143891759 0.000000e+00 7736.0
1 TraesCS2D01G197200 chr2D 84.664 1102 82 31 2608 3698 623404544 623403519 0.000000e+00 1018.0
2 TraesCS2D01G197200 chr2D 89.691 194 16 1 1 190 518024800 518024993 1.160000e-60 244.0
3 TraesCS2D01G197200 chr2D 83.111 225 30 4 2244 2462 623404808 623404586 9.190000e-47 198.0
4 TraesCS2D01G197200 chr2B 92.770 3430 150 44 796 4189 202157340 202153973 0.000000e+00 4870.0
5 TraesCS2D01G197200 chr2B 90.952 630 27 11 197 802 202166751 202166128 0.000000e+00 821.0
6 TraesCS2D01G197200 chr2A 91.387 2798 152 35 1029 3760 157534520 157537294 0.000000e+00 3749.0
7 TraesCS2D01G197200 chr2A 84.557 1185 93 34 2523 3697 81460063 81461167 0.000000e+00 1092.0
8 TraesCS2D01G197200 chr2A 86.039 881 72 23 2827 3697 43917515 43916676 0.000000e+00 898.0
9 TraesCS2D01G197200 chr2A 85.235 596 36 24 239 796 157533440 157534021 2.190000e-157 566.0
10 TraesCS2D01G197200 chr2A 91.346 312 21 5 3883 4189 157537341 157537651 5.010000e-114 422.0
11 TraesCS2D01G197200 chr2A 84.332 434 26 16 2522 2953 765404785 765405178 1.830000e-103 387.0
12 TraesCS2D01G197200 chr2A 84.956 226 24 6 2244 2462 81459843 81460065 1.960000e-53 220.0
13 TraesCS2D01G197200 chr2A 85.714 203 21 4 2244 2440 43918144 43917944 1.530000e-49 207.0
14 TraesCS2D01G197200 chr2A 95.745 47 2 0 822 868 157534013 157534059 4.490000e-10 76.8
15 TraesCS2D01G197200 chr5D 84.287 1101 87 30 2608 3698 488187158 488186134 0.000000e+00 996.0
16 TraesCS2D01G197200 chr5D 83.111 225 30 4 2244 2462 488187422 488187200 9.190000e-47 198.0
17 TraesCS2D01G197200 chr1B 83.005 1118 102 43 2593 3698 20776998 20775957 0.000000e+00 931.0
18 TraesCS2D01G197200 chr1B 84.812 902 86 31 2808 3698 20803326 20802465 0.000000e+00 859.0
19 TraesCS2D01G197200 chr1B 88.670 203 17 4 1 198 682295589 682295388 4.180000e-60 243.0
20 TraesCS2D01G197200 chr1B 83.556 225 29 5 2244 2462 20803720 20803498 1.970000e-48 204.0
21 TraesCS2D01G197200 chr6D 85.017 901 80 19 2809 3698 79935881 79936737 0.000000e+00 865.0
22 TraesCS2D01G197200 chr6D 90.722 194 14 1 1 190 346275560 346275753 5.370000e-64 255.0
23 TraesCS2D01G197200 chr6D 89.796 196 17 2 1 193 283794100 283794295 8.990000e-62 248.0
24 TraesCS2D01G197200 chr6D 86.076 79 7 3 3774 3852 473093032 473092958 9.650000e-12 82.4
25 TraesCS2D01G197200 chr1A 84.101 434 27 16 2522 2953 251370308 251370701 8.500000e-102 381.0
26 TraesCS2D01G197200 chr1A 84.101 434 27 18 2522 2953 540637035 540637428 8.500000e-102 381.0
27 TraesCS2D01G197200 chr1A 94.175 103 4 1 2244 2346 251368979 251369079 5.610000e-34 156.0
28 TraesCS2D01G197200 chr3A 90.909 198 14 1 1 194 674130137 674130334 3.210000e-66 263.0
29 TraesCS2D01G197200 chr7D 91.192 193 14 2 1 190 8874042 8874234 4.150000e-65 259.0
30 TraesCS2D01G197200 chr7D 89.848 197 14 4 1 193 484323440 484323246 8.990000e-62 248.0
31 TraesCS2D01G197200 chr1D 90.722 194 14 2 1 190 387058602 387058795 5.370000e-64 255.0
32 TraesCS2D01G197200 chr4B 88.350 206 17 3 1 201 645295185 645294982 1.500000e-59 241.0
33 TraesCS2D01G197200 chr6B 94.175 103 4 1 2244 2346 22933698 22933798 5.610000e-34 156.0
34 TraesCS2D01G197200 chr4A 84.932 73 3 1 3788 3852 696013843 696013771 2.700000e-07 67.6
35 TraesCS2D01G197200 chrUn 82.143 84 8 5 3777 3853 352728773 352728856 9.720000e-07 65.8
36 TraesCS2D01G197200 chrUn 82.143 84 8 5 3777 3853 407129600 407129517 9.720000e-07 65.8
37 TraesCS2D01G197200 chrUn 100.000 33 0 0 3821 3853 299704257 299704289 1.260000e-05 62.1
38 TraesCS2D01G197200 chr6A 95.238 42 1 1 3809 3850 411084938 411084898 9.720000e-07 65.8
39 TraesCS2D01G197200 chr3D 82.143 84 8 5 3777 3853 29510456 29510373 9.720000e-07 65.8
40 TraesCS2D01G197200 chr3D 82.143 84 8 5 3777 3853 29547168 29547085 9.720000e-07 65.8
41 TraesCS2D01G197200 chr3D 82.143 84 8 5 3777 3853 29549878 29549795 9.720000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G197200 chr2D 143891759 143895947 4188 True 7736.00 7736 100.00000 1 4189 1 chr2D.!!$R1 4188
1 TraesCS2D01G197200 chr2D 623403519 623404808 1289 True 608.00 1018 83.88750 2244 3698 2 chr2D.!!$R2 1454
2 TraesCS2D01G197200 chr2B 202153973 202157340 3367 True 4870.00 4870 92.77000 796 4189 1 chr2B.!!$R1 3393
3 TraesCS2D01G197200 chr2B 202166128 202166751 623 True 821.00 821 90.95200 197 802 1 chr2B.!!$R2 605
4 TraesCS2D01G197200 chr2A 157533440 157537651 4211 False 1203.45 3749 90.92825 239 4189 4 chr2A.!!$F3 3950
5 TraesCS2D01G197200 chr2A 81459843 81461167 1324 False 656.00 1092 84.75650 2244 3697 2 chr2A.!!$F2 1453
6 TraesCS2D01G197200 chr2A 43916676 43918144 1468 True 552.50 898 85.87650 2244 3697 2 chr2A.!!$R1 1453
7 TraesCS2D01G197200 chr5D 488186134 488187422 1288 True 597.00 996 83.69900 2244 3698 2 chr5D.!!$R1 1454
8 TraesCS2D01G197200 chr1B 20775957 20776998 1041 True 931.00 931 83.00500 2593 3698 1 chr1B.!!$R1 1105
9 TraesCS2D01G197200 chr1B 20802465 20803720 1255 True 531.50 859 84.18400 2244 3698 2 chr1B.!!$R3 1454
10 TraesCS2D01G197200 chr6D 79935881 79936737 856 False 865.00 865 85.01700 2809 3698 1 chr6D.!!$F1 889
11 TraesCS2D01G197200 chr1A 251368979 251370701 1722 False 268.50 381 89.13800 2244 2953 2 chr1A.!!$F2 709

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
176 177 0.033090 CGGGGGTAGGATAAAGTCGC 59.967 60.0 0.00 0.00 0.0 5.19 F
177 178 0.033090 GGGGGTAGGATAAAGTCGCG 59.967 60.0 0.00 0.00 0.0 5.87 F
182 183 0.248743 TAGGATAAAGTCGCGCGGTG 60.249 55.0 31.69 1.17 0.0 4.94 F
413 427 0.391661 TCAGATTTCACGGCCAGCTC 60.392 55.0 2.24 0.00 0.0 4.09 F
2046 2439 0.609131 CGGAGAAGGCAATGGTGGTT 60.609 55.0 0.00 0.00 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2511 2.415608 GCCGTCCTCGATGGTCTCA 61.416 63.158 2.02 0.00 40.59 3.27 R
2235 2628 2.258591 GAGAGCGCAACGAGTGGA 59.741 61.111 11.47 0.00 0.00 4.02 R
2297 2692 4.951715 AGCATAACATTTGCAATGAGAGGA 59.048 37.500 0.00 0.00 42.62 3.71 R
2406 3934 2.241722 CAATGACGGTCGCATCAAAAC 58.758 47.619 3.34 0.00 0.00 2.43 R
3894 5689 0.250424 TCATGACCACACCACAGCTG 60.250 55.000 13.48 13.48 0.00 4.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.719616 GCGCGCTGTCCGTTTCAC 62.720 66.667 26.67 0.00 39.71 3.18
40 41 4.072088 CGCGCTGTCCGTTTCACC 62.072 66.667 5.56 0.00 39.71 4.02
41 42 3.723348 GCGCTGTCCGTTTCACCC 61.723 66.667 0.00 0.00 39.71 4.61
42 43 3.047877 CGCTGTCCGTTTCACCCC 61.048 66.667 0.00 0.00 0.00 4.95
43 44 2.112297 GCTGTCCGTTTCACCCCA 59.888 61.111 0.00 0.00 0.00 4.96
44 45 1.527380 GCTGTCCGTTTCACCCCAA 60.527 57.895 0.00 0.00 0.00 4.12
45 46 1.104577 GCTGTCCGTTTCACCCCAAA 61.105 55.000 0.00 0.00 0.00 3.28
46 47 1.394618 CTGTCCGTTTCACCCCAAAA 58.605 50.000 0.00 0.00 0.00 2.44
47 48 1.066454 CTGTCCGTTTCACCCCAAAAC 59.934 52.381 0.00 0.00 34.09 2.43
48 49 0.386476 GTCCGTTTCACCCCAAAACC 59.614 55.000 0.00 0.00 33.93 3.27
49 50 0.033405 TCCGTTTCACCCCAAAACCA 60.033 50.000 0.00 0.00 33.93 3.67
50 51 0.387565 CCGTTTCACCCCAAAACCAG 59.612 55.000 0.00 0.00 33.93 4.00
51 52 0.249280 CGTTTCACCCCAAAACCAGC 60.249 55.000 0.00 0.00 33.93 4.85
52 53 0.249280 GTTTCACCCCAAAACCAGCG 60.249 55.000 0.00 0.00 31.80 5.18
53 54 2.022240 TTTCACCCCAAAACCAGCGC 62.022 55.000 0.00 0.00 0.00 5.92
54 55 3.222855 CACCCCAAAACCAGCGCA 61.223 61.111 11.47 0.00 0.00 6.09
55 56 2.443016 ACCCCAAAACCAGCGCAA 60.443 55.556 11.47 0.00 0.00 4.85
56 57 2.060980 ACCCCAAAACCAGCGCAAA 61.061 52.632 11.47 0.00 0.00 3.68
57 58 1.594021 CCCCAAAACCAGCGCAAAC 60.594 57.895 11.47 0.00 0.00 2.93
58 59 1.441311 CCCAAAACCAGCGCAAACT 59.559 52.632 11.47 0.00 0.00 2.66
59 60 0.179086 CCCAAAACCAGCGCAAACTT 60.179 50.000 11.47 0.00 0.00 2.66
60 61 0.929615 CCAAAACCAGCGCAAACTTG 59.070 50.000 11.47 6.23 0.00 3.16
61 62 0.929615 CAAAACCAGCGCAAACTTGG 59.070 50.000 11.47 11.09 37.98 3.61
62 63 0.820871 AAAACCAGCGCAAACTTGGA 59.179 45.000 18.50 0.00 35.89 3.53
63 64 0.102300 AAACCAGCGCAAACTTGGAC 59.898 50.000 18.50 0.00 35.89 4.02
64 65 1.034838 AACCAGCGCAAACTTGGACA 61.035 50.000 18.50 0.00 35.89 4.02
65 66 1.283793 CCAGCGCAAACTTGGACAG 59.716 57.895 11.47 0.00 33.76 3.51
66 67 1.283793 CAGCGCAAACTTGGACAGG 59.716 57.895 11.47 0.00 0.00 4.00
67 68 1.898574 AGCGCAAACTTGGACAGGG 60.899 57.895 11.47 0.00 0.00 4.45
68 69 2.919494 GCGCAAACTTGGACAGGGG 61.919 63.158 0.30 0.00 0.00 4.79
69 70 1.228124 CGCAAACTTGGACAGGGGA 60.228 57.895 0.00 0.00 0.00 4.81
70 71 0.609131 CGCAAACTTGGACAGGGGAT 60.609 55.000 0.00 0.00 0.00 3.85
71 72 0.890683 GCAAACTTGGACAGGGGATG 59.109 55.000 0.00 0.00 0.00 3.51
73 74 1.888512 CAAACTTGGACAGGGGATGTG 59.111 52.381 0.00 0.00 44.17 3.21
74 75 1.149101 AACTTGGACAGGGGATGTGT 58.851 50.000 0.00 0.00 44.17 3.72
75 76 0.693049 ACTTGGACAGGGGATGTGTC 59.307 55.000 0.00 0.00 44.17 3.67
76 77 0.391661 CTTGGACAGGGGATGTGTCG 60.392 60.000 0.00 0.00 44.17 4.35
77 78 0.834261 TTGGACAGGGGATGTGTCGA 60.834 55.000 0.00 0.00 44.17 4.20
78 79 0.834261 TGGACAGGGGATGTGTCGAA 60.834 55.000 0.00 0.00 44.17 3.71
79 80 0.323629 GGACAGGGGATGTGTCGAAA 59.676 55.000 0.00 0.00 44.17 3.46
80 81 1.676014 GGACAGGGGATGTGTCGAAAG 60.676 57.143 0.00 0.00 44.17 2.62
81 82 0.321653 ACAGGGGATGTGTCGAAAGC 60.322 55.000 0.00 0.00 41.91 3.51
82 83 1.079127 AGGGGATGTGTCGAAAGCG 60.079 57.895 0.00 0.00 39.35 4.68
83 84 2.106683 GGGGATGTGTCGAAAGCGG 61.107 63.158 0.00 0.00 38.28 5.52
84 85 1.079405 GGGATGTGTCGAAAGCGGA 60.079 57.895 0.00 0.00 38.28 5.54
85 86 1.359459 GGGATGTGTCGAAAGCGGAC 61.359 60.000 0.00 0.00 38.28 4.79
86 87 0.669318 GGATGTGTCGAAAGCGGACA 60.669 55.000 0.00 0.00 38.28 4.02
87 88 0.438830 GATGTGTCGAAAGCGGACAC 59.561 55.000 19.53 19.53 42.92 3.67
88 89 1.142097 TGTGTCGAAAGCGGACACA 59.858 52.632 22.90 22.90 46.18 3.72
89 90 0.460459 TGTGTCGAAAGCGGACACAA 60.460 50.000 23.85 13.36 45.81 3.33
90 91 0.653636 GTGTCGAAAGCGGACACAAA 59.346 50.000 20.67 0.00 42.55 2.83
91 92 1.062880 GTGTCGAAAGCGGACACAAAA 59.937 47.619 20.67 0.00 42.55 2.44
92 93 1.062880 TGTCGAAAGCGGACACAAAAC 59.937 47.619 0.00 0.00 38.28 2.43
93 94 0.302288 TCGAAAGCGGACACAAAACG 59.698 50.000 0.00 0.00 38.28 3.60
94 95 0.656205 CGAAAGCGGACACAAAACGG 60.656 55.000 0.00 0.00 0.00 4.44
95 96 0.658897 GAAAGCGGACACAAAACGGA 59.341 50.000 0.00 0.00 0.00 4.69
96 97 0.379316 AAAGCGGACACAAAACGGAC 59.621 50.000 0.00 0.00 0.00 4.79
97 98 0.745128 AAGCGGACACAAAACGGACA 60.745 50.000 0.00 0.00 0.00 4.02
98 99 0.745128 AGCGGACACAAAACGGACAA 60.745 50.000 0.00 0.00 0.00 3.18
99 100 0.099082 GCGGACACAAAACGGACAAA 59.901 50.000 0.00 0.00 0.00 2.83
100 101 1.858399 GCGGACACAAAACGGACAAAG 60.858 52.381 0.00 0.00 0.00 2.77
101 102 1.666700 CGGACACAAAACGGACAAAGA 59.333 47.619 0.00 0.00 0.00 2.52
102 103 2.289547 CGGACACAAAACGGACAAAGAT 59.710 45.455 0.00 0.00 0.00 2.40
103 104 3.606153 CGGACACAAAACGGACAAAGATC 60.606 47.826 0.00 0.00 0.00 2.75
104 105 3.304458 GGACACAAAACGGACAAAGATCC 60.304 47.826 0.00 0.00 35.16 3.36
111 112 3.676091 GGACAAAGATCCGTTTGCG 57.324 52.632 7.21 0.00 40.49 4.85
112 113 0.454452 GGACAAAGATCCGTTTGCGC 60.454 55.000 0.00 0.00 40.49 6.09
113 114 0.454452 GACAAAGATCCGTTTGCGCC 60.454 55.000 4.18 0.00 40.49 6.53
114 115 1.154035 CAAAGATCCGTTTGCGCCC 60.154 57.895 4.18 0.00 36.67 6.13
115 116 2.686816 AAAGATCCGTTTGCGCCCG 61.687 57.895 4.18 4.36 36.67 6.13
136 137 3.423154 GCTGGGCCGTCTCGTTTG 61.423 66.667 0.00 0.00 0.00 2.93
137 138 3.423154 CTGGGCCGTCTCGTTTGC 61.423 66.667 0.00 0.00 0.00 3.68
141 142 4.699522 GCCGTCTCGTTTGCCCCT 62.700 66.667 0.00 0.00 0.00 4.79
142 143 2.032071 CCGTCTCGTTTGCCCCTT 59.968 61.111 0.00 0.00 0.00 3.95
143 144 1.599797 CCGTCTCGTTTGCCCCTTT 60.600 57.895 0.00 0.00 0.00 3.11
144 145 1.170290 CCGTCTCGTTTGCCCCTTTT 61.170 55.000 0.00 0.00 0.00 2.27
145 146 1.515081 CGTCTCGTTTGCCCCTTTTA 58.485 50.000 0.00 0.00 0.00 1.52
146 147 1.196127 CGTCTCGTTTGCCCCTTTTAC 59.804 52.381 0.00 0.00 0.00 2.01
147 148 1.538512 GTCTCGTTTGCCCCTTTTACC 59.461 52.381 0.00 0.00 0.00 2.85
148 149 1.422402 TCTCGTTTGCCCCTTTTACCT 59.578 47.619 0.00 0.00 0.00 3.08
149 150 1.810755 CTCGTTTGCCCCTTTTACCTC 59.189 52.381 0.00 0.00 0.00 3.85
150 151 1.143277 TCGTTTGCCCCTTTTACCTCA 59.857 47.619 0.00 0.00 0.00 3.86
151 152 1.957877 CGTTTGCCCCTTTTACCTCAA 59.042 47.619 0.00 0.00 0.00 3.02
152 153 2.362717 CGTTTGCCCCTTTTACCTCAAA 59.637 45.455 0.00 0.00 0.00 2.69
153 154 3.724374 GTTTGCCCCTTTTACCTCAAAC 58.276 45.455 0.00 0.00 37.29 2.93
154 155 1.611519 TGCCCCTTTTACCTCAAACG 58.388 50.000 0.00 0.00 0.00 3.60
155 156 1.143277 TGCCCCTTTTACCTCAAACGA 59.857 47.619 0.00 0.00 0.00 3.85
156 157 2.232399 GCCCCTTTTACCTCAAACGAA 58.768 47.619 0.00 0.00 0.00 3.85
157 158 2.030540 GCCCCTTTTACCTCAAACGAAC 60.031 50.000 0.00 0.00 0.00 3.95
158 159 2.224784 CCCCTTTTACCTCAAACGAACG 59.775 50.000 0.00 0.00 0.00 3.95
159 160 2.224784 CCCTTTTACCTCAAACGAACGG 59.775 50.000 0.00 0.00 0.00 4.44
160 161 2.224784 CCTTTTACCTCAAACGAACGGG 59.775 50.000 0.00 0.00 0.00 5.28
161 162 1.881591 TTTACCTCAAACGAACGGGG 58.118 50.000 0.00 0.00 0.00 5.73
162 163 0.035176 TTACCTCAAACGAACGGGGG 59.965 55.000 0.00 0.00 0.00 5.40
163 164 1.120795 TACCTCAAACGAACGGGGGT 61.121 55.000 0.00 0.00 0.00 4.95
164 165 1.120795 ACCTCAAACGAACGGGGGTA 61.121 55.000 0.00 0.00 0.00 3.69
165 166 0.390735 CCTCAAACGAACGGGGGTAG 60.391 60.000 0.00 0.00 0.00 3.18
166 167 0.390735 CTCAAACGAACGGGGGTAGG 60.391 60.000 0.00 0.00 0.00 3.18
167 168 0.831288 TCAAACGAACGGGGGTAGGA 60.831 55.000 0.00 0.00 0.00 2.94
168 169 0.251073 CAAACGAACGGGGGTAGGAT 59.749 55.000 0.00 0.00 0.00 3.24
169 170 1.481772 CAAACGAACGGGGGTAGGATA 59.518 52.381 0.00 0.00 0.00 2.59
170 171 1.864669 AACGAACGGGGGTAGGATAA 58.135 50.000 0.00 0.00 0.00 1.75
171 172 1.864669 ACGAACGGGGGTAGGATAAA 58.135 50.000 0.00 0.00 0.00 1.40
172 173 1.758862 ACGAACGGGGGTAGGATAAAG 59.241 52.381 0.00 0.00 0.00 1.85
173 174 1.758862 CGAACGGGGGTAGGATAAAGT 59.241 52.381 0.00 0.00 0.00 2.66
174 175 2.223900 CGAACGGGGGTAGGATAAAGTC 60.224 54.545 0.00 0.00 0.00 3.01
175 176 1.406903 ACGGGGGTAGGATAAAGTCG 58.593 55.000 0.00 0.00 0.00 4.18
176 177 0.033090 CGGGGGTAGGATAAAGTCGC 59.967 60.000 0.00 0.00 0.00 5.19
177 178 0.033090 GGGGGTAGGATAAAGTCGCG 59.967 60.000 0.00 0.00 0.00 5.87
178 179 0.599466 GGGGTAGGATAAAGTCGCGC 60.599 60.000 0.00 0.00 0.00 6.86
179 180 0.938168 GGGTAGGATAAAGTCGCGCG 60.938 60.000 26.76 26.76 0.00 6.86
180 181 0.938168 GGTAGGATAAAGTCGCGCGG 60.938 60.000 31.69 11.75 0.00 6.46
181 182 0.248784 GTAGGATAAAGTCGCGCGGT 60.249 55.000 31.69 15.43 0.00 5.68
182 183 0.248743 TAGGATAAAGTCGCGCGGTG 60.249 55.000 31.69 1.17 0.00 4.94
183 184 2.522638 GGATAAAGTCGCGCGGTGG 61.523 63.158 31.69 0.71 0.00 4.61
184 185 1.517694 GATAAAGTCGCGCGGTGGA 60.518 57.895 31.69 7.56 0.00 4.02
185 186 1.480219 GATAAAGTCGCGCGGTGGAG 61.480 60.000 31.69 0.00 0.00 3.86
186 187 2.221906 ATAAAGTCGCGCGGTGGAGT 62.222 55.000 31.69 10.72 0.00 3.85
187 188 2.424705 TAAAGTCGCGCGGTGGAGTT 62.425 55.000 31.69 16.66 0.00 3.01
195 196 4.003788 CGGTGGAGTTGGGCTCGT 62.004 66.667 0.00 0.00 45.03 4.18
226 227 2.167281 CCCACAATCAAACCACAACACA 59.833 45.455 0.00 0.00 0.00 3.72
235 236 4.605967 CACAACACACGCGCACCC 62.606 66.667 5.73 0.00 0.00 4.61
274 276 1.454539 CTTTTGACCCCCGAGTGGT 59.545 57.895 0.00 0.00 39.32 4.16
285 287 4.141642 ACCCCCGAGTGGTTATTATTACAC 60.142 45.833 0.00 0.00 29.75 2.90
364 370 1.670590 GCTGCCTGACTGACTGACT 59.329 57.895 0.00 0.00 0.00 3.41
389 395 4.398598 CGGGAAAAAGCCGCACCG 62.399 66.667 0.00 0.00 35.01 4.94
412 426 0.392193 CTCAGATTTCACGGCCAGCT 60.392 55.000 2.24 0.00 0.00 4.24
413 427 0.391661 TCAGATTTCACGGCCAGCTC 60.392 55.000 2.24 0.00 0.00 4.09
414 428 1.448540 AGATTTCACGGCCAGCTCG 60.449 57.895 2.24 0.00 0.00 5.03
415 429 3.100862 GATTTCACGGCCAGCTCGC 62.101 63.158 2.24 0.00 0.00 5.03
487 514 2.169663 GTGTCACACGATACGACGAT 57.830 50.000 0.00 0.00 37.03 3.73
625 673 2.943978 CGCTTTCCTCCCCGACTGT 61.944 63.158 0.00 0.00 0.00 3.55
717 775 3.423154 GCGACAAGTGCGGGAAGG 61.423 66.667 0.00 0.00 0.00 3.46
718 776 3.423154 CGACAAGTGCGGGAAGGC 61.423 66.667 0.00 0.00 0.00 4.35
719 777 3.056328 GACAAGTGCGGGAAGGCC 61.056 66.667 0.00 0.00 0.00 5.19
820 878 2.202892 GCTCCCCATTCCGTCGTC 60.203 66.667 0.00 0.00 0.00 4.20
946 1012 2.485795 CCCAACCACCAACACACCG 61.486 63.158 0.00 0.00 0.00 4.94
1692 2085 3.184683 GCGCTGCTCAACCTCTCG 61.185 66.667 0.00 0.00 0.00 4.04
2046 2439 0.609131 CGGAGAAGGCAATGGTGGTT 60.609 55.000 0.00 0.00 0.00 3.67
2184 2577 2.668889 GCTCTGCTGCAGCTGTGT 60.669 61.111 36.61 0.00 42.66 3.72
2297 2692 5.815740 CCAAGCACAAGGTATACGTTCTAAT 59.184 40.000 7.83 0.00 0.00 1.73
2406 3934 4.962155 ACTTGTCAGTCTAAGGTTTGAGG 58.038 43.478 0.00 0.00 0.00 3.86
2419 3947 2.607038 GGTTTGAGGTTTTGATGCGACC 60.607 50.000 0.00 0.00 0.00 4.79
2430 3958 0.928229 GATGCGACCGTCATTGTACC 59.072 55.000 0.00 0.00 0.00 3.34
2440 3968 2.798283 CGTCATTGTACCGAACAGTGTT 59.202 45.455 8.61 8.61 44.08 3.32
2451 3979 3.001838 CCGAACAGTGTTCAACGAATTCA 59.998 43.478 30.17 0.00 0.00 2.57
2644 4193 4.153117 CAGGTGTTGACTTGTAGATTCAGC 59.847 45.833 0.00 0.00 0.00 4.26
2743 4326 3.100671 GGAAGTACAGGAGGATGAGTGT 58.899 50.000 0.00 0.00 0.00 3.55
2744 4327 3.515901 GGAAGTACAGGAGGATGAGTGTT 59.484 47.826 0.00 0.00 0.00 3.32
2823 4408 1.074319 TCGTAAACGATGCTCGGTGC 61.074 55.000 0.14 0.00 39.92 5.01
2887 4641 3.190118 GTGCTTGAGATTTCCCACTGAAG 59.810 47.826 0.00 0.00 33.63 3.02
2966 4723 7.341030 TGTCATGACTAATTTGATCCTCATGT 58.659 34.615 25.55 0.00 37.40 3.21
2975 4732 3.998913 TGATCCTCATGTGTGCCTTAA 57.001 42.857 0.00 0.00 0.00 1.85
2979 4736 5.357878 TGATCCTCATGTGTGCCTTAATTTC 59.642 40.000 0.00 0.00 0.00 2.17
2983 4740 6.267471 TCCTCATGTGTGCCTTAATTTCTTTT 59.733 34.615 0.00 0.00 0.00 2.27
2984 4741 6.930722 CCTCATGTGTGCCTTAATTTCTTTTT 59.069 34.615 0.00 0.00 0.00 1.94
2985 4742 7.116805 CCTCATGTGTGCCTTAATTTCTTTTTC 59.883 37.037 0.00 0.00 0.00 2.29
2986 4743 6.928492 TCATGTGTGCCTTAATTTCTTTTTCC 59.072 34.615 0.00 0.00 0.00 3.13
2987 4744 5.285651 TGTGTGCCTTAATTTCTTTTTCCG 58.714 37.500 0.00 0.00 0.00 4.30
2997 4754 6.516739 AATTTCTTTTTCCGAAGAGGGATC 57.483 37.500 0.00 0.00 41.52 3.36
2998 4755 3.247006 TCTTTTTCCGAAGAGGGATCG 57.753 47.619 0.00 0.00 41.52 3.69
3088 4846 8.177663 CCACTTATATGTTCAGTTGTGTGATTC 58.822 37.037 0.00 0.00 0.00 2.52
3304 5063 1.424493 CGCCGGCTCTGTTCTTGATC 61.424 60.000 26.68 0.00 0.00 2.92
3308 5067 0.537188 GGCTCTGTTCTTGATCCGGA 59.463 55.000 6.61 6.61 0.00 5.14
3329 5088 1.908299 TCGAGAACAGAGCAGCCCA 60.908 57.895 0.00 0.00 0.00 5.36
3489 5253 3.898741 CCAGGTTATCTTAGGAGAGGACC 59.101 52.174 0.00 0.00 39.39 4.46
3521 5292 2.488153 CTCAGTATGTGTGGTGTCGAGA 59.512 50.000 0.00 0.00 37.40 4.04
3539 5310 3.242903 CGAGATGTAGCTGTGTACAGGAG 60.243 52.174 13.41 0.00 43.94 3.69
3571 5343 2.872842 GCGGTAATATGGTAATGCCGGT 60.873 50.000 1.90 0.00 41.21 5.28
3584 5356 2.961768 CCGGTTTGGCTTTGCGAT 59.038 55.556 0.00 0.00 0.00 4.58
3604 5376 4.997395 CGATGTTATAGGGGAATGTTGGAG 59.003 45.833 0.00 0.00 0.00 3.86
3605 5377 4.788925 TGTTATAGGGGAATGTTGGAGG 57.211 45.455 0.00 0.00 0.00 4.30
3772 5551 2.488153 GGCACTCAGACCATTTAACACC 59.512 50.000 0.00 0.00 0.00 4.16
3779 5558 6.724905 ACTCAGACCATTTAACACCTACTACT 59.275 38.462 0.00 0.00 0.00 2.57
3880 5660 4.074970 CTGATGTAACCCATATGGAAGCC 58.925 47.826 24.00 8.68 37.39 4.35
3885 5665 1.601759 CCCATATGGAAGCCGCTGG 60.602 63.158 24.00 0.00 37.39 4.85
3894 5689 1.569479 GAAGCCGCTGGTTCACTGAC 61.569 60.000 14.23 0.00 45.99 3.51
3900 5695 3.694364 CTGGTTCACTGACAGCTGT 57.306 52.632 21.88 21.88 0.00 4.40
3942 5738 1.290203 CAGCTATCGCGAACCAATGT 58.710 50.000 15.24 0.00 42.32 2.71
3945 5741 4.234574 CAGCTATCGCGAACCAATGTATA 58.765 43.478 15.24 0.00 42.32 1.47
3983 5780 4.873817 TGGTTGCACTCAAGAATTCATTG 58.126 39.130 8.44 9.34 31.93 2.82
3989 5786 6.849502 TGCACTCAAGAATTCATTGAAGATC 58.150 36.000 8.44 6.13 36.30 2.75
4062 5861 0.389948 GCTGTCCCGACTACTGGTTG 60.390 60.000 0.00 0.00 0.00 3.77
4081 5880 2.710220 GCTGATGCAACACATGAACA 57.290 45.000 0.00 0.00 39.84 3.18
4132 5931 1.080569 CAAGGGTTCGTGCAATGCC 60.081 57.895 1.53 0.00 0.00 4.40
4151 5950 0.460311 CGGTGATAGGTTTCGGCTCT 59.540 55.000 0.00 0.00 0.00 4.09
4178 5977 3.066190 CTCCAGACCGGCGGTACA 61.066 66.667 34.29 14.79 35.25 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.719616 GTGAAACGGACAGCGCGC 62.720 66.667 26.66 26.66 0.00 6.86
23 24 4.072088 GGTGAAACGGACAGCGCG 62.072 66.667 0.00 0.00 38.12 6.86
24 25 3.723348 GGGTGAAACGGACAGCGC 61.723 66.667 0.00 0.00 38.12 5.92
25 26 3.047877 GGGGTGAAACGGACAGCG 61.048 66.667 0.00 0.00 38.12 5.18
26 27 1.104577 TTTGGGGTGAAACGGACAGC 61.105 55.000 0.00 0.00 38.12 4.40
27 28 1.066454 GTTTTGGGGTGAAACGGACAG 59.934 52.381 0.00 0.00 38.12 3.51
28 29 1.104630 GTTTTGGGGTGAAACGGACA 58.895 50.000 0.00 0.00 38.12 4.02
29 30 0.386476 GGTTTTGGGGTGAAACGGAC 59.614 55.000 0.00 0.00 37.76 4.79
30 31 0.033405 TGGTTTTGGGGTGAAACGGA 60.033 50.000 0.00 0.00 37.76 4.69
31 32 0.387565 CTGGTTTTGGGGTGAAACGG 59.612 55.000 0.00 0.00 37.76 4.44
32 33 0.249280 GCTGGTTTTGGGGTGAAACG 60.249 55.000 0.00 0.00 37.76 3.60
33 34 0.249280 CGCTGGTTTTGGGGTGAAAC 60.249 55.000 0.00 0.00 36.51 2.78
34 35 2.022240 GCGCTGGTTTTGGGGTGAAA 62.022 55.000 0.00 0.00 0.00 2.69
35 36 2.494530 GCGCTGGTTTTGGGGTGAA 61.495 57.895 0.00 0.00 0.00 3.18
36 37 2.909965 GCGCTGGTTTTGGGGTGA 60.910 61.111 0.00 0.00 0.00 4.02
37 38 2.303549 TTTGCGCTGGTTTTGGGGTG 62.304 55.000 9.73 0.00 0.00 4.61
38 39 2.060980 TTTGCGCTGGTTTTGGGGT 61.061 52.632 9.73 0.00 0.00 4.95
39 40 1.594021 GTTTGCGCTGGTTTTGGGG 60.594 57.895 9.73 0.00 0.00 4.96
40 41 0.179086 AAGTTTGCGCTGGTTTTGGG 60.179 50.000 9.73 0.00 0.00 4.12
41 42 0.929615 CAAGTTTGCGCTGGTTTTGG 59.070 50.000 9.73 0.00 0.00 3.28
42 43 0.929615 CCAAGTTTGCGCTGGTTTTG 59.070 50.000 9.73 7.07 0.00 2.44
43 44 0.820871 TCCAAGTTTGCGCTGGTTTT 59.179 45.000 9.73 0.00 0.00 2.43
44 45 0.102300 GTCCAAGTTTGCGCTGGTTT 59.898 50.000 9.73 0.00 0.00 3.27
45 46 1.034838 TGTCCAAGTTTGCGCTGGTT 61.035 50.000 9.73 0.00 0.00 3.67
46 47 1.447317 CTGTCCAAGTTTGCGCTGGT 61.447 55.000 9.73 0.00 0.00 4.00
47 48 1.283793 CTGTCCAAGTTTGCGCTGG 59.716 57.895 9.73 7.76 0.00 4.85
48 49 1.283793 CCTGTCCAAGTTTGCGCTG 59.716 57.895 9.73 0.00 0.00 5.18
49 50 1.898574 CCCTGTCCAAGTTTGCGCT 60.899 57.895 9.73 0.00 0.00 5.92
50 51 2.644992 CCCTGTCCAAGTTTGCGC 59.355 61.111 0.00 0.00 0.00 6.09
51 52 0.609131 ATCCCCTGTCCAAGTTTGCG 60.609 55.000 0.00 0.00 0.00 4.85
52 53 0.890683 CATCCCCTGTCCAAGTTTGC 59.109 55.000 0.00 0.00 0.00 3.68
53 54 1.888512 CACATCCCCTGTCCAAGTTTG 59.111 52.381 0.00 0.00 35.29 2.93
54 55 1.499007 ACACATCCCCTGTCCAAGTTT 59.501 47.619 0.00 0.00 35.29 2.66
55 56 1.073923 GACACATCCCCTGTCCAAGTT 59.926 52.381 0.00 0.00 35.29 2.66
56 57 0.693049 GACACATCCCCTGTCCAAGT 59.307 55.000 0.00 0.00 35.29 3.16
57 58 0.391661 CGACACATCCCCTGTCCAAG 60.392 60.000 0.00 0.00 35.29 3.61
58 59 0.834261 TCGACACATCCCCTGTCCAA 60.834 55.000 0.00 0.00 35.29 3.53
59 60 0.834261 TTCGACACATCCCCTGTCCA 60.834 55.000 0.00 0.00 35.29 4.02
60 61 0.323629 TTTCGACACATCCCCTGTCC 59.676 55.000 0.00 0.00 35.29 4.02
61 62 1.726853 CTTTCGACACATCCCCTGTC 58.273 55.000 0.00 0.00 35.29 3.51
62 63 0.321653 GCTTTCGACACATCCCCTGT 60.322 55.000 0.00 0.00 39.20 4.00
63 64 1.361668 CGCTTTCGACACATCCCCTG 61.362 60.000 0.00 0.00 38.10 4.45
64 65 1.079127 CGCTTTCGACACATCCCCT 60.079 57.895 0.00 0.00 38.10 4.79
65 66 2.106683 CCGCTTTCGACACATCCCC 61.107 63.158 0.00 0.00 38.10 4.81
66 67 1.079405 TCCGCTTTCGACACATCCC 60.079 57.895 0.00 0.00 38.10 3.85
67 68 0.669318 TGTCCGCTTTCGACACATCC 60.669 55.000 0.00 0.00 38.10 3.51
68 69 0.438830 GTGTCCGCTTTCGACACATC 59.561 55.000 14.49 0.00 41.65 3.06
69 70 0.249699 TGTGTCCGCTTTCGACACAT 60.250 50.000 17.34 0.00 44.00 3.21
70 71 0.460459 TTGTGTCCGCTTTCGACACA 60.460 50.000 17.34 17.34 45.45 3.72
71 72 0.653636 TTTGTGTCCGCTTTCGACAC 59.346 50.000 12.91 12.91 41.99 3.67
72 73 1.062880 GTTTTGTGTCCGCTTTCGACA 59.937 47.619 0.00 0.00 38.10 4.35
73 74 1.738432 GTTTTGTGTCCGCTTTCGAC 58.262 50.000 0.00 0.00 38.10 4.20
74 75 0.302288 CGTTTTGTGTCCGCTTTCGA 59.698 50.000 0.00 0.00 38.10 3.71
75 76 0.656205 CCGTTTTGTGTCCGCTTTCG 60.656 55.000 0.00 0.00 0.00 3.46
76 77 0.658897 TCCGTTTTGTGTCCGCTTTC 59.341 50.000 0.00 0.00 0.00 2.62
77 78 0.379316 GTCCGTTTTGTGTCCGCTTT 59.621 50.000 0.00 0.00 0.00 3.51
78 79 0.745128 TGTCCGTTTTGTGTCCGCTT 60.745 50.000 0.00 0.00 0.00 4.68
79 80 0.745128 TTGTCCGTTTTGTGTCCGCT 60.745 50.000 0.00 0.00 0.00 5.52
80 81 0.099082 TTTGTCCGTTTTGTGTCCGC 59.901 50.000 0.00 0.00 0.00 5.54
81 82 1.666700 TCTTTGTCCGTTTTGTGTCCG 59.333 47.619 0.00 0.00 0.00 4.79
82 83 3.304458 GGATCTTTGTCCGTTTTGTGTCC 60.304 47.826 0.00 0.00 0.00 4.02
83 84 3.885358 GGATCTTTGTCCGTTTTGTGTC 58.115 45.455 0.00 0.00 0.00 3.67
84 85 3.982576 GGATCTTTGTCCGTTTTGTGT 57.017 42.857 0.00 0.00 0.00 3.72
93 94 0.454452 GCGCAAACGGATCTTTGTCC 60.454 55.000 0.30 0.00 40.57 4.02
94 95 0.454452 GGCGCAAACGGATCTTTGTC 60.454 55.000 10.83 2.83 40.57 3.18
95 96 1.579429 GGCGCAAACGGATCTTTGT 59.421 52.632 10.83 0.00 40.57 2.83
96 97 1.154035 GGGCGCAAACGGATCTTTG 60.154 57.895 10.83 3.64 40.57 2.77
97 98 2.686816 CGGGCGCAAACGGATCTTT 61.687 57.895 10.83 0.00 40.57 2.52
98 99 3.124921 CGGGCGCAAACGGATCTT 61.125 61.111 10.83 0.00 40.57 2.40
119 120 3.423154 CAAACGAGACGGCCCAGC 61.423 66.667 0.00 0.00 0.00 4.85
120 121 3.423154 GCAAACGAGACGGCCCAG 61.423 66.667 0.00 0.00 0.00 4.45
124 125 4.699522 AGGGGCAAACGAGACGGC 62.700 66.667 0.00 0.00 0.00 5.68
125 126 1.170290 AAAAGGGGCAAACGAGACGG 61.170 55.000 0.00 0.00 0.00 4.79
126 127 1.196127 GTAAAAGGGGCAAACGAGACG 59.804 52.381 0.00 0.00 0.00 4.18
127 128 1.538512 GGTAAAAGGGGCAAACGAGAC 59.461 52.381 0.00 0.00 0.00 3.36
128 129 1.422402 AGGTAAAAGGGGCAAACGAGA 59.578 47.619 0.00 0.00 0.00 4.04
129 130 1.810755 GAGGTAAAAGGGGCAAACGAG 59.189 52.381 0.00 0.00 0.00 4.18
130 131 1.143277 TGAGGTAAAAGGGGCAAACGA 59.857 47.619 0.00 0.00 0.00 3.85
131 132 1.611519 TGAGGTAAAAGGGGCAAACG 58.388 50.000 0.00 0.00 0.00 3.60
132 133 3.724374 GTTTGAGGTAAAAGGGGCAAAC 58.276 45.455 0.00 0.00 38.52 2.93
133 134 2.362717 CGTTTGAGGTAAAAGGGGCAAA 59.637 45.455 0.00 0.00 0.00 3.68
134 135 1.957877 CGTTTGAGGTAAAAGGGGCAA 59.042 47.619 0.00 0.00 0.00 4.52
135 136 1.143277 TCGTTTGAGGTAAAAGGGGCA 59.857 47.619 0.00 0.00 0.00 5.36
136 137 1.900245 TCGTTTGAGGTAAAAGGGGC 58.100 50.000 0.00 0.00 0.00 5.80
137 138 2.224784 CGTTCGTTTGAGGTAAAAGGGG 59.775 50.000 0.00 0.00 0.00 4.79
138 139 2.224784 CCGTTCGTTTGAGGTAAAAGGG 59.775 50.000 0.00 0.00 0.00 3.95
139 140 2.224784 CCCGTTCGTTTGAGGTAAAAGG 59.775 50.000 0.00 0.00 0.00 3.11
140 141 2.224784 CCCCGTTCGTTTGAGGTAAAAG 59.775 50.000 0.00 0.00 0.00 2.27
141 142 2.220313 CCCCGTTCGTTTGAGGTAAAA 58.780 47.619 0.00 0.00 0.00 1.52
142 143 1.542987 CCCCCGTTCGTTTGAGGTAAA 60.543 52.381 0.00 0.00 0.00 2.01
143 144 0.035176 CCCCCGTTCGTTTGAGGTAA 59.965 55.000 0.00 0.00 0.00 2.85
144 145 1.120795 ACCCCCGTTCGTTTGAGGTA 61.121 55.000 0.00 0.00 0.00 3.08
145 146 1.120795 TACCCCCGTTCGTTTGAGGT 61.121 55.000 0.00 0.00 0.00 3.85
146 147 0.390735 CTACCCCCGTTCGTTTGAGG 60.391 60.000 0.00 0.00 0.00 3.86
147 148 0.390735 CCTACCCCCGTTCGTTTGAG 60.391 60.000 0.00 0.00 0.00 3.02
148 149 0.831288 TCCTACCCCCGTTCGTTTGA 60.831 55.000 0.00 0.00 0.00 2.69
149 150 0.251073 ATCCTACCCCCGTTCGTTTG 59.749 55.000 0.00 0.00 0.00 2.93
150 151 1.864669 TATCCTACCCCCGTTCGTTT 58.135 50.000 0.00 0.00 0.00 3.60
151 152 1.864669 TTATCCTACCCCCGTTCGTT 58.135 50.000 0.00 0.00 0.00 3.85
152 153 1.758862 CTTTATCCTACCCCCGTTCGT 59.241 52.381 0.00 0.00 0.00 3.85
153 154 1.758862 ACTTTATCCTACCCCCGTTCG 59.241 52.381 0.00 0.00 0.00 3.95
154 155 2.223900 CGACTTTATCCTACCCCCGTTC 60.224 54.545 0.00 0.00 0.00 3.95
155 156 1.758862 CGACTTTATCCTACCCCCGTT 59.241 52.381 0.00 0.00 0.00 4.44
156 157 1.406903 CGACTTTATCCTACCCCCGT 58.593 55.000 0.00 0.00 0.00 5.28
157 158 0.033090 GCGACTTTATCCTACCCCCG 59.967 60.000 0.00 0.00 0.00 5.73
158 159 0.033090 CGCGACTTTATCCTACCCCC 59.967 60.000 0.00 0.00 0.00 5.40
159 160 0.599466 GCGCGACTTTATCCTACCCC 60.599 60.000 12.10 0.00 0.00 4.95
160 161 0.938168 CGCGCGACTTTATCCTACCC 60.938 60.000 28.94 0.00 0.00 3.69
161 162 0.938168 CCGCGCGACTTTATCCTACC 60.938 60.000 34.63 0.00 0.00 3.18
162 163 0.248784 ACCGCGCGACTTTATCCTAC 60.249 55.000 34.63 0.00 0.00 3.18
163 164 0.248743 CACCGCGCGACTTTATCCTA 60.249 55.000 34.63 0.00 0.00 2.94
164 165 1.518572 CACCGCGCGACTTTATCCT 60.519 57.895 34.63 0.00 0.00 3.24
165 166 2.522638 CCACCGCGCGACTTTATCC 61.523 63.158 34.63 0.00 0.00 2.59
166 167 1.480219 CTCCACCGCGCGACTTTATC 61.480 60.000 34.63 0.00 0.00 1.75
167 168 1.518572 CTCCACCGCGCGACTTTAT 60.519 57.895 34.63 6.07 0.00 1.40
168 169 2.126228 CTCCACCGCGCGACTTTA 60.126 61.111 34.63 11.52 0.00 1.85
169 170 3.802418 AACTCCACCGCGCGACTTT 62.802 57.895 34.63 12.14 0.00 2.66
170 171 4.295119 AACTCCACCGCGCGACTT 62.295 61.111 34.63 12.58 0.00 3.01
178 179 2.558554 CTACGAGCCCAACTCCACCG 62.559 65.000 0.00 0.00 43.01 4.94
179 180 1.218316 CTACGAGCCCAACTCCACC 59.782 63.158 0.00 0.00 43.01 4.61
180 181 0.173708 CTCTACGAGCCCAACTCCAC 59.826 60.000 0.00 0.00 43.01 4.02
181 182 2.579878 CTCTACGAGCCCAACTCCA 58.420 57.895 0.00 0.00 43.01 3.86
214 215 2.101380 GCGCGTGTGTTGTGGTTT 59.899 55.556 8.43 0.00 0.00 3.27
235 236 3.733344 ATCATCACGGGGGCGTTCG 62.733 63.158 0.00 0.00 0.00 3.95
274 276 5.217393 CGCCTCGCAGTAGTGTAATAATAA 58.783 41.667 0.00 0.00 0.00 1.40
285 287 1.959899 CTTTGCACGCCTCGCAGTAG 61.960 60.000 0.00 0.00 41.18 2.57
364 370 2.438795 CTTTTTCCCGGGGGAGCA 59.561 61.111 23.50 0.00 46.06 4.26
389 395 3.093278 CCGTGAAATCTGAGCCGC 58.907 61.111 0.00 0.00 0.00 6.53
440 455 4.214327 CTTCGAGCTCCGCCTCCC 62.214 72.222 8.47 0.00 38.37 4.30
473 495 1.298116 CGGCATCGTCGTATCGTGT 60.298 57.895 0.00 0.00 0.00 4.49
717 775 1.716172 GCTGAAAATCTCGTCCGGC 59.284 57.895 0.00 0.00 0.00 6.13
718 776 1.421410 CCGCTGAAAATCTCGTCCGG 61.421 60.000 0.00 0.00 0.00 5.14
719 777 0.457853 TCCGCTGAAAATCTCGTCCG 60.458 55.000 0.00 0.00 0.00 4.79
722 780 1.078759 CGCTCCGCTGAAAATCTCGT 61.079 55.000 0.00 0.00 0.00 4.18
723 781 1.078759 ACGCTCCGCTGAAAATCTCG 61.079 55.000 0.00 0.00 0.00 4.04
946 1012 0.842635 AGTGATGATGAAGGGAGGGC 59.157 55.000 0.00 0.00 0.00 5.19
1248 1641 2.579738 GAGGAGGACTTGGCGACC 59.420 66.667 0.00 0.00 0.00 4.79
1293 1686 3.003763 AAGTCCCGGGACAGCTCC 61.004 66.667 46.20 25.33 46.76 4.70
1704 2097 2.867472 GTGATGGCCGAACGGTTG 59.133 61.111 14.63 0.00 37.65 3.77
1773 2166 2.486966 GCATTCTGCTTGGCCGAC 59.513 61.111 0.00 0.00 40.96 4.79
1776 2169 4.503314 GCGGCATTCTGCTTGGCC 62.503 66.667 0.00 0.00 44.28 5.36
1866 2259 4.468615 GAGAGCAGCGCGACGAGT 62.469 66.667 12.10 0.00 0.00 4.18
2046 2439 4.399395 CTGGCGAGGCTGGCAAGA 62.399 66.667 20.13 3.62 44.45 3.02
2082 2475 4.641645 CCGGCTTCCACCACAGCA 62.642 66.667 0.00 0.00 37.81 4.41
2118 2511 2.415608 GCCGTCCTCGATGGTCTCA 61.416 63.158 2.02 0.00 40.59 3.27
2235 2628 2.258591 GAGAGCGCAACGAGTGGA 59.741 61.111 11.47 0.00 0.00 4.02
2297 2692 4.951715 AGCATAACATTTGCAATGAGAGGA 59.048 37.500 0.00 0.00 42.62 3.71
2406 3934 2.241722 CAATGACGGTCGCATCAAAAC 58.758 47.619 3.34 0.00 0.00 2.43
2419 3947 2.400399 ACACTGTTCGGTACAATGACG 58.600 47.619 3.25 0.00 36.02 4.35
2430 3958 4.190304 TGAATTCGTTGAACACTGTTCG 57.810 40.909 15.60 6.34 0.00 3.95
2440 3968 7.655732 TCAAACTCTAACTGATGAATTCGTTGA 59.344 33.333 0.77 0.00 0.00 3.18
2451 3979 6.591834 CGGACTTCAATCAAACTCTAACTGAT 59.408 38.462 0.00 0.00 0.00 2.90
2488 4016 6.367969 CCGGTCCAGAGTTAATATATTTTCCG 59.632 42.308 2.68 0.00 0.00 4.30
2644 4193 3.055591 GTGCATATCTCGACCATGTGAG 58.944 50.000 0.00 0.00 0.00 3.51
2743 4326 3.351740 CTGTAGGAGAGAGAGCACTCAA 58.648 50.000 13.86 0.00 44.79 3.02
2744 4327 2.356638 CCTGTAGGAGAGAGAGCACTCA 60.357 54.545 13.86 0.00 40.58 3.41
2823 4408 7.486802 TTTAAGTTTCCTCGTTTTCTAGTGG 57.513 36.000 0.00 0.00 0.00 4.00
2887 4641 8.719478 ATAATTATAAGCACGTACACGAGTAC 57.281 34.615 12.51 12.51 45.67 2.73
2966 4723 5.776173 TCGGAAAAAGAAATTAAGGCACA 57.224 34.783 0.00 0.00 0.00 4.57
2975 4732 4.636206 CGATCCCTCTTCGGAAAAAGAAAT 59.364 41.667 0.00 0.00 34.95 2.17
2979 4736 1.666189 GCGATCCCTCTTCGGAAAAAG 59.334 52.381 0.00 0.00 37.10 2.27
2983 4740 2.805546 CGCGATCCCTCTTCGGAA 59.194 61.111 0.00 0.00 37.10 4.30
2984 4741 3.900892 GCGCGATCCCTCTTCGGA 61.901 66.667 12.10 0.00 37.10 4.55
2985 4742 4.207281 TGCGCGATCCCTCTTCGG 62.207 66.667 12.10 0.00 37.10 4.30
2986 4743 2.956964 GTGCGCGATCCCTCTTCG 60.957 66.667 12.10 0.00 39.55 3.79
2987 4744 2.586357 GGTGCGCGATCCCTCTTC 60.586 66.667 12.10 0.00 0.00 2.87
3088 4846 2.230994 TAGCAAGGTCTCAGCCTGCG 62.231 60.000 0.00 0.00 39.17 5.18
3191 4949 2.434185 TTCGTCGCATGACCAGCC 60.434 61.111 0.00 0.00 42.37 4.85
3304 5063 1.134901 CTCTGTTCTCGACGTCCGG 59.865 63.158 10.58 0.00 39.14 5.14
3308 5067 1.081108 GCTGCTCTGTTCTCGACGT 60.081 57.895 0.00 0.00 0.00 4.34
3329 5088 0.677731 CATCGCGCCCCATCCATATT 60.678 55.000 0.00 0.00 0.00 1.28
3489 5253 3.005554 CACATACTGAGAAGCAACCCAG 58.994 50.000 0.00 0.00 0.00 4.45
3521 5292 2.821437 ACCTCCTGTACACAGCTACAT 58.179 47.619 3.75 0.00 42.47 2.29
3539 5310 4.019950 ACCATATTACCGCCCTAACATACC 60.020 45.833 0.00 0.00 0.00 2.73
3571 5343 3.380004 CCCTATAACATCGCAAAGCCAAA 59.620 43.478 0.00 0.00 0.00 3.28
3584 5356 3.461831 CCCTCCAACATTCCCCTATAACA 59.538 47.826 0.00 0.00 0.00 2.41
3640 5412 1.341976 CGGAACAAGGGGGATTTGGAT 60.342 52.381 0.00 0.00 0.00 3.41
3825 5605 6.860080 TCCCTCTGTAAACTAATACAAGACG 58.140 40.000 0.00 0.00 35.48 4.18
3826 5606 7.760340 CACTCCCTCTGTAAACTAATACAAGAC 59.240 40.741 0.00 0.00 35.48 3.01
3831 5611 9.363763 GTAAACACTCCCTCTGTAAACTAATAC 57.636 37.037 0.00 0.00 0.00 1.89
3880 5660 3.248029 GCTGTCAGTGAACCAGCG 58.752 61.111 17.11 0.00 41.80 5.18
3885 5665 0.940126 CACCACAGCTGTCAGTGAAC 59.060 55.000 30.12 0.00 37.97 3.18
3889 5669 1.146930 CCACACCACAGCTGTCAGT 59.853 57.895 18.64 14.92 0.00 3.41
3890 5670 0.882042 GACCACACCACAGCTGTCAG 60.882 60.000 18.64 14.20 0.00 3.51
3891 5671 1.146041 GACCACACCACAGCTGTCA 59.854 57.895 18.64 0.00 0.00 3.58
3894 5689 0.250424 TCATGACCACACCACAGCTG 60.250 55.000 13.48 13.48 0.00 4.24
3900 5695 3.326297 TGTTAGTGATCATGACCACACCA 59.674 43.478 22.38 11.95 35.84 4.17
3983 5780 0.394080 AGCCAGCCAGCTTGATCTTC 60.394 55.000 0.00 0.00 41.41 2.87
3989 5786 0.393402 TATGACAGCCAGCCAGCTTG 60.393 55.000 0.00 0.00 42.61 4.01
4062 5861 2.710220 TGTTCATGTGTTGCATCAGC 57.290 45.000 0.00 0.00 42.57 4.26
4081 5880 2.105766 GGCTGGCATTCCTGATCTTTT 58.894 47.619 0.00 0.00 33.56 2.27
4132 5931 0.460311 AGAGCCGAAACCTATCACCG 59.540 55.000 0.00 0.00 0.00 4.94


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.